If you don't use PortalID and ModuleID, every instance of your new module will be exactly the same, winhin the portal and across all portals that are being hosted by DotNetNuke. In addition, you may want your module to appear differently based on something other than module settings. It would be like having a Text/HTML module with preloaded text that always appears the same on any page on any portal. You can display the module on every page of your site if you wish with standard modules settings but I have rarely seen it used in actual portals.

If you are only going to use one portal you may not need the PortalID. If you to intend to use the same module on more than one page (as per usual) you must use the ModuleID.

It is quite difficult for me to imagine your database schema, but perhaps I can explain it in another way.

A moduleID is reference to an instance of a module, somewhat like an item's storage location in a warehouse. The location id is always the same, but an item cam be moved to a different location just by changing the item.location.

In the case of DotNetNuke, a ModuleID is issued when you add a new module. When you add that module to a page, it is referenced by the ModuleID. DNN uses this technique so that you can use the same base module on different pages, each with its own unique settings.

The bottom line is that if you are developing a module, you should follow the best practice that DNN has already implemented for you. Does that make more sense?